[gmx-users] Re: gmx-users Digest, Vol 75, Issue 107

Tue Jul 20 15:41:51 CEST 2010


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Sent: Tuesday, July 20, 2010 1:00 PM
To: <gmx-users at gromacs.org>
Subject: gmx-users Digest, Vol 75, Issue 107

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> Today's Topics:
>
>   1. selenomethionine parameters for ffG53a6 (Deniz KARASU)
>   2. Re: Tabulated potentials and performance (Lanyuan Lu)
>   3. Heme_Grompp Error (shahid nayeem)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Mon, 19 Jul 2010 22:24:13 +0300
> From: Deniz KARASU <karasudeniz at gmail.com>
> Subject: [gmx-users] selenomethionine parameters for ffG53a6
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTil1ezcaZAP1Fgx75B4KD1ikwClcVlEMza5pR0Nf at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hi all,
>
>
> Where can I find selenomethionine parameters for ffG53a6 forcefield?
>
> Deniz.
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> ------------------------------
>
> Message: 2
> Date: Mon, 19 Jul 2010 17:18:02 -0500
> From: Lanyuan Lu <lulanyuanhec at gmail.com>
> Subject: Re: [gmx-users] Tabulated potentials and performance
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTim3TJvATjAK-0Cshvx-r2CA4SHwNFQB3qM4QzMq at mail.gmail.com>
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>
>>From our group's experience, there is a critical point for dramatic
> performance drop when one uses two many tables. The possible reason is 
> that
> the size of tables exceeds the cache size. However, this only happens when
> the number of tables is beyond something like 50. The total table size for
> the critical point can depend on the hardware condition.
> Lanyuan
>
> On Mon, Jul 19, 2010 at 1:49 PM, ms <devicerandom at gmail.com> wrote:
>
>> On 19/07/10 18:32, Da-Wei Li wrote:
>>
>>> I remember the manu states that it won't cost too much compared with
>>> standard potential function form.
>>>
>>
>> Well, I find in the manual exactly the opposite:
>> "Note that table lookup is signiï¬cantly slower than computation of the 
>> most
>> simple Lennard-Jones and Coulomb interaction." (p.133)
>>
>> But I am already using tables for most nonbonded interactions and the
>> performance is OK. What I would like to know is, if I increase the 
>> *number
>> of tables* (keeping the number of particles/interactions the same, but, 
>> say,
>> using two tables where I used only one before), is it going to be
>> significantly worse or not?
>>
>> thanks!
>>
>> m.
>>
>>
>>  dawei
>>>
>>> On Mon, Jul 19, 2010 at 1:22 PM, ms<devicerandom at gmail.com>  wrote:
>>>
>>>> On 19/07/10 17:32, Da-Wei Li wrote:
>>>>
>>>>>
>>>>> It will be very little from my experience. Remember that the dominate
>>>>> part is the non-bonded force calculation.
>>>>>
>>>>
>>>> Well, that's exactly what I tabulate.
>>>>
>>>>
>>>>> dawei
>>>>>
>>>>> On Mon, Jul 19, 2010 at 12:22 PM, ms<devicerandom at gmail.com>    wrote:
>>>>>
>>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> Do you know where can I find some information on how using tabulated
>>>>>> potential affects gmx performance, and how? I have to decide how to
>>>>>> project
>>>>>> a custom model but I don't want to calculate dozens of tables only to
>>>>>> find
>>>>>> that gmx grinds to a halt.
>>>>>>
>>>>>> thanks!
>>>>>> M.
>>>>>> --
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> Message: 3
> Date: Tue, 20 Jul 2010 09:41:56 +0530
> From: shahid nayeem <msnayeem at gmail.com>
> Subject: [gmx-users] Heme_Grompp Error
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID:
> <AANLkTim5iZz2utUIFJNI26g4GlyZdoLQKhCAX5Kaq0Wl at mail.gmail.com>
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>
> Dear All
> I used the following command sequentially to prepare file for energy
> minimization and subsequent MD run.
> 1. pdb2gmx  -f *.pdb -o seq.gro -p seq.top
> 2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
> 3. genbox   -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p seq.top
> 4. grompp   -c seq_b4ion.gro -p seq.top -o seq_b4ion.tpr -f em.mdp
> grompp gives following error.processing topology...
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1nb.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ffG43a1bon.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
> Generated 279 of the 1225 non-bonded parameter combinations
>
> ERROR 1 [file seq.top, line 1965]:
> No default G96Bond types
>
>
> ERROR 2 [file seq.top, line 5271]:
> No default G96Angle types
>
>
> ERROR 3 [file seq.top, line 5272]:
> No default G96Angle types
>
>
> ERROR 4 [file seq.top, line 5648]:
> No default G96Angle types
>
>
> ERROR 5 [file seq.top, line 5653]:
> No default G96Angle types
>
>
> ERROR 6 [file seq.top, line 5654]:
> No default G96Angle types
>
>
> ERROR 7 [file seq.top, line 5655]:
> No default G96Angle types
>
>
> ERROR 8 [file seq.top, line 5656]:
> No default G96Angle types
>
>
> ERROR 9 [file seq.top, line 6201]:
> No default Proper Dih. types
>
> Opening library file /usr/local/gromacs/share/gromacs/top/spc.itp
> Opening library file /usr/local/gromacs/share/gromacs/top/ions.itp
> Excluding 3 bonded neighbours molecule type 'Protein_A'
> Excluding 2 bonded neighbours molecule type 'SOL'
> Excluding 2 bonded neighbours molecule type 'SOL'
>
> NOTE 1 [file seq.top, line 6932]:
> System has non-zero total charge: 7.000001e+00
>
>
>
> processing coordinates...
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
>
> There was 1 note
>
> -------------------------------------------------------
> Program grompp, VERSION 4.0.7
> Source code file: grompp.c, line: 986
>
> Fatal error:
> There were 9 errors in input file(s)
> -------------------------------------------------------
> pdb2gmx works properly using ff43a1 forcefield. My protein contains
> Heme.  This heme is bonded to MET SD and NE2 HIS as well as NA NB NC ND of
> heme porphyrins. It is actually these six bond which is created in 
> topology
> file with pdb2gmx using specbond.dat, giving error in grompp. I tried to
> find these bonds in in built files of gromacs i.e. /share/top/ but I
> couldnt. Can any one help me and tell me where can I find these 
> bonds/angle
> parameters and what should I add in ffG43a1 .itp .rtp files
> please help.
> Shahid Nayeem
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